R/mongo_constructors.R
In mariyad/openbiodiving: Linking the Open Biodiversity Knowledge Management System With BOLD Systems to Retrieve Specimen Voucher Metadata
#' @export
metadata = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
pub_date = function(year, month, day) {
literal(paste0(text_value = unlist(year)["text_value"],
"-", unlist(month)["text_value"], "-", unlist(day)["text_value"]),
xsd_type = rdf4r::xsd_date)
}
if (length(atoms$pensoft_pub) > 0) {
stop("Pensoft publication")
}
#query mongo for research paper
general_collection = mongolite::mongo("new_collection")
# print(unlist(atoms$doi)["text_value"])
doi = unlist(atoms$doi)["text_value"]
paper_key = check_mongo(value = doi, type = "research_paper", collection = general_collection, regex = FALSE)
if (is.null(paper_key)==TRUE){
#if there is no research paper id, create it and save it in the collection
paper_key = set_obkms("taxpub_research_paper", "research_paper")
save_to_mongo(key = paper_key, value = doi, type = "research_paper", collection = general_collection)
}
paper_id = identifier(paper_key)
article_id = identifiers$root_id
#query mongo for publisher id
publisher_lit = unlist(atoms$publisher)["text_value"]
publisher_key = check_mongo(value = publisher_lit, type = "publisher", collection = general_collection, regex = FALSE)
if (is.null(publisher_key)==TRUE){
#if there is no research paper id, create it and save it in the collection
publisher_key = set_obkms("taxpub_publisher", "publisher")
save_to_mongo(key = publisher_key, value = publisher_lit, type = "publisher", collection = general_collection)
}
publisher_id = identifier(publisher_key)
#query mongo for journal id
journal_lit = unlist(atoms$journal)["text_value"]
journal_key = check_mongo(value = journal_lit, type = "journal", collection = general_collection, regex = FALSE)
if (is.null(journal_key)==TRUE){
#if there is no research paper id, create it and save it in the collection
journal_key = set_obkms("taxpub_journal", "journal")
save_to_mongo(key = journal_key, value = journal_lit, type = "journal", collection = general_collection)
}
journal_id = identifier(journal_key)
tt = ResourceDescriptionFramework$new()
tt$add_triple(journal_id, rdf_type, Journal)
sapply(atoms$journal, function(j) {
tt$add_triple(journal_id, pref_label, j)
})
sapply(atoms$journal_abbrev, function(j) {
tt$add_triple(journal_id, alt_label, j)
})
sapply(atoms$issn, function(i) {
tt$add_triple(journal_id, issn, i)
})
sapply(atoms$eIssn, function(i) {
tt$add_triple(journal_id, eissn, i)
})
tt$add_triple(journal_id, frbr_part, article_id)
tt$add_triple(article_id, rdf_type, Article)
sapply(atoms$title, function(i) {
tt$add_triple(article_id, rdfs_label, i)
})
sapply(atoms$title, function(i) {
tt$add_triple(article_id, dc_title, i)
})
sapply(atoms$doi, function(i) {
tt$add_triple(article_id, has_doi, i)
})
sapply(atoms$publisher, function(i) {
tt$add_triple(article_id, has_publisher, i)
})
sapply(atoms$date, function(i) {
tt$add_triple(article_id, publication_date, i)
})
sapply(list(pub_date(atoms$pub_year, atoms$pub_month, atoms$pub_day)),
function(i) {
tt$add_triple(article_id, publication_date, i)
})
tt$add_triple(article_id, has_publisher_id, publisher_id)
tt$add_triple(article_id, realization_of, paper_id)
sapply(atoms$issue, function(i) {
tt$add_triple(article_id, has_issue, i)
})
sapply(atoms$keyword, function(i) {
tt$add_triple(identifiers$nid, has_keyword, i)
})
tt$add_triple(publisher_id, rdf_type, Publisher)
sapply(atoms$publisher, function(i) {
tt$add_triple(publisher_id, rdfs_label, i)
})
tt$add_triple(paper_id, rdf_type, Paper)
return(tt)
}
#' @export
keyword_group = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, KeywordGroup)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$keyword, function(i) {
tt$add_triple(identifiers$nid, has_keyword, i)
})
return(tt)
}
#' @export
abstract = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, Abstract)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
sapply(atoms$trans_abstract, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
title = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, Title)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
author_new = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
full_name = function(lsurname, lgiven_name) {
if (length(lsurname) == 1 && length(lgiven_name) == 1) {
paste(lgiven_name[[1]]$text_value, lsurname[[1]]$text_value)
}
else if (length(lsurname) == 1) {
lsurname[[1]]$text_value
}
else {
NA
}
}
atoms$full_name = ifelse(length(atoms$full_name) == 0, list(literal(full_name(atoms$surname,
atoms$given_names), xsd_type = rdf4r::xsd_string)), atoms$full_name)
aid = sapply(atoms$aff_id, function(a) {
as.integer(gsub("[^0-9.]", "", a$text_value))
})
paper_id = identifiers$root_id
author_id = identifiers$nid
#concatenate affiliation institution and city
all_affs = NULL
for(r in 1:length(atoms$all_affiliations_institutions)){
a = paste0(atoms$all_affiliations_institutions[[r]]$text_value, ",", atoms$all_affiliations_cities[[r]]$text_value)
a = literal(a, xsd_type = rdf4r::xsd_string)
all_affs[[r]] = a
}
tt = ResourceDescriptionFramework$new()
tt$add_triple(paper_id, creator, author_id)
tt$add_triple(author_id, rdf_type, Person)
sapply(atoms$full_name, function(j) {
tt$add_triple(author_id, rdfs_label, j)
})
sapply(all_affs[aid], function(j) {
tt$add_triple(author_id, has_affiliation, j)
})
sapply(atoms$email, function(j) {
tt$add_triple(author_id, has_email, j)
})
return(tt)
}
#' @export
introduction_section = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, Introduction)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
discussion = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, Discussion)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
treatment_new = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
#lookup_taxonomic_concept = query_factory(p_query = qlookup_taxonomic_concept_id,
# access_options = access_options)
#openbiodiv_taxonomic_concept_id = identifier_factory(fun = list(lookup_taxonomic_concept),
# prefixes = access_options$prefix, def_prefix = access_options$prefix["openbiodiv"], schema_name = schema_name, mongo_key = mongo_key)
treatment_id = identifiers$nid
#check mongo collection for treatments+tc (treatment frbf:realizationof taxonomicConcept)
treatment_collection = mongolite::mongo("treatment_collection")
key = check_mongo(value = treatment_id$id, type = names(mongo_key), collection = treatment_collection, regex = FALSE)
if (is.null(key)){
#if there is no tc realization of the treatment, create it
key = set_obkms("taxonomic_concept", names(mongo_key))
#save it both in the treatment collection and in the general collection
general_collection = mongolite::mongo("new_collection")
save_to_mongo(key, treatment_id$id, names(mongo_key), treatment_collection)
save_to_mongo(key, treatment_id$id, "taxonomic_concept", general_collection)
}
taxonomic_concept_id = identifier(id = key, prefix = prefix)
#taxonomic_concept_id = openbiodiv_taxonomic_concept_id(list(treatment_id))
tt = ResourceDescriptionFramework$new()
tt$add_triple(treatment_id, rdf_type, Treatment)
tt$add_triple(treatment_id, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(treatment_id, has_content, i)
})
tt$add_triple(taxonomic_concept_id, rdf_type, TaxonomicConcept)
tt$add_triple(taxonomic_concept_id, realization, treatment_id)
return(tt)
}
#' @export
nomenclature_citations = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, NomenclatureCitationsList)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
nomenclature = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
nomenclature_id = identifiers$nid
tt = ResourceDescriptionFramework$new()
tt$add_triple(nomenclature_id, rdf_type, Nomenclature)
tt$add_triple(nomenclature_id, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(nomenclature_id, has_content, i)
})
return(tt)
}
#' @export
materials_examined = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, MaterialsExamined)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
diagnosis = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
diagnosis_id = identifiers$nid
tt = ResourceDescriptionFramework$new()
tt$add_triple(diagnosis_id, rdf_type, Diagnosis)
tt$add_triple(diagnosis_id, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(diagnosis_id, has_content, i)
})
return(tt)
}
#' @export
distribution = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, Distribution)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
taxonomic_key = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, TaxonomicKey)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
figure = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, Figure)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
taxonomic_name_usage_new = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
taxon_id = identifiers$nid
# print(taxon_id)
atoml_to_val = function(atoml)
{
if (length(atoml) > 0) {
return(atoml[[1]]$text_value)
}
else {
return (NA)
}
}
# identifiers
label = literal(get_scientific_name_or_tcl(kingdom = atoml_to_val(atoms$kingdom),
phylum = atoml_to_val(atoms$phylum),
class = atoml_to_val(atoms$class),
order = atoml_to_val(atoms$order),
family = atoml_to_val(atoms$family),
subfamily = atoml_to_val(atoms$subfamily),
genus = atoml_to_val(atoms$genus),
subgenus = atoml_to_val(atoms$subgenus),
species = atoml_to_val(atoms$species),
subspecies = atoml_to_val(atoms$subspecies),
authorship = atoml_to_val(atoms$authorship),
secundum_literal = atoml_to_val(atoms$secundum_literal)))
if (is.null(label) && length(atoms$verbatim) >= 1)
{
label = atoms$verbatim[[1]]
}
if (is.null(label))
{
return(ResourceDescriptionFramework$new())
}
if (length(atoms$verbatim_status) >= 1) {
atoms$status = list(verbstat2openbiodiv(atoms$verbatim_status[[1]]$text_value,
def_prefix = access_options$prefix))
}
rank = function(kingdom = NA, phylum = NA, class = NA, order = NA,
family = NA, subfamily = NA, genus = NA, subgenus = NA,
species = NA, subspecies = NA) {
arglist = list(Kingdom = kingdom, Phylum = phylum, Class = class,
Order = order, Family = family, Subfamily = subfamily,
Genus = genus, Subgenus = subgenus, Species = species,
Subspecies = subspecies)
identifier(id = names(arglist)[max(sapply(1:length(arglist),
function(index) {
ifelse(has_meaningful_value(arglist[[index]]),
index, 0)
}))], prefix = access_options$prefix)
}
atoms$taxonomic_rank = list(rank(kingdom = atoml_to_val(atoms$kingdom),
phylum = atoml_to_val(atoms$phylum), class = atoml_to_val(atoms$class),
order = atoml_to_val(atoms$order), family = atoml_to_val(atoms$family),
subfamily = atoml_to_val(atoms$subfamily), genus = atoml_to_val(atoms$genus),
subgenus = atoml_to_val(atoms$subgenus), species = atoml_to_val(atoms$species),
subspecies = atoml_to_val(atoms$subspecies)))
if (length(atoms$regularzied_genus) > 0) {
atoms$genus = atoms$regularzied_genus
}
#find the tnu_id by looking at mongo collection for tnus
tnu_collection = mongolite::mongo("tnus")
label = label[!is.null(label)]
paper_id = stringr::str_extract(identifiers$root_id$id, "([^\\/]*)$")
#HERE DO A REGEX SEARCH
mongo_tnu = check_mongo(paper_id, label$text_value, tnu_collection, regex = FALSE)
#if there is no tnu there, create it and save it
if (is.null(mongo_tnu)){
#create id and save the tnu
mongo_tnu = set_obkms(schema_name, "tnu")
label = as.character(label$text_value)
save_to_mongo(key = mongo_tnu, value = paper_id , type = label, collection = tnu_collection)
}
#if there is id, jsut take it
tnu_id = identifier(mongo_tnu)
todate = function(year, month, day) {
list(literal(paste(year[[1]]$text_value, month[[1]]$text_value,
day[[1]]$text_value, sep = "-"), xsd_type = rdf4r::xsd_date))
}
atoms$date = append(atoms$date, todate(atoms$pub_year, atoms$pub_month,
atoms$pub_day))
article_id = identifiers$root_id
parent_element_id = identifiers$pid
tt = ResourceDescriptionFramework$new()
tt$add_triple(tnu_id, rdf_type, TaxonomicNameUsage)
tt$add_triple(tnu_id, mentions, taxon_id)
tt$add_triple(tnu_id, is_contained_by, parent_element_id)
sapply(atoms$date, function(i) {
tt$add_triple(tnu_id, publication_date, i)
})
sapply(atoms$verbatim_status, function(i) {
tt$add_triple(tnu_id, has_taxonomic_status, i)
})
sapply(atoms$status, function(i) {
tt$add_triple(tnu_id, has_taxonomic_status_id, i)
})
tt$add_triple(taxon_id, rdf_type, ScientificName)
tt$add_triple(taxon_id, rdfs_label, label)
tt$add_triple(taxon_id, has_scientific_name, label)
sapply(atoms$kingdom, function(i) {
tt$add_triple(taxon_id, dwc_kingdom, i)
})
sapply(atoms$phylum, function(i) {
tt$add_triple(taxon_id, dwc_phylum, i)
})
sapply(atoms$class, function(i) {
tt$add_triple(taxon_id, dwc_class, i)
})
sapply(atoms$order, function(i) {
tt$add_triple(taxon_id, dwc_order, i)
})
sapply(atoms$family, function(i) {
tt$add_triple(taxon_id, dwc_family, i)
})
sapply(atoms$subfamily, function(i) {
tt$add_triple(taxon_id, dwc_family, i)
})
sapply(atoms$genus, function(i) {
tt$add_triple(taxon_id, dwc_genus, i)
})
sapply(atoms$subgenus, function(i) {
tt$add_triple(taxon_id, dwc_subgenus, i)
})
sapply(atoms$species, function(i) {
tt$add_triple(taxon_id, dwc_species_ep, i)
})
sapply(atoms$subspecies, function(i) {
tt$add_triple(taxon_id, dwc_subspecies_ep, i)
})
sapply(atoms$verbatim_rank, function(i) {
tt$add_triple(taxon_id, has_verbatim_rank, i)
})
sapply(atoms$taxonomic_rank, function(i) {
tt$add_triple(taxon_id, has_taxonomic_rank_id,
i)
})
sapply(atoms$authorship, function(i) {
tt$add_triple(taxon_id, dwc_authorship, i)
})
return(tt)
}
mariyad/openbiodiving documentation built on June 3, 2019, 2:18 p.m.
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#' @export
metadata = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
pub_date = function(year, month, day) {
literal(paste0(text_value = unlist(year)["text_value"],
"-", unlist(month)["text_value"], "-", unlist(day)["text_value"]),
xsd_type = rdf4r::xsd_date)
}
if (length(atoms$pensoft_pub) > 0) {
stop("Pensoft publication")
}
#query mongo for research paper
general_collection = mongolite::mongo("new_collection")
# print(unlist(atoms$doi)["text_value"])
doi = unlist(atoms$doi)["text_value"]
paper_key = check_mongo(value = doi, type = "research_paper", collection = general_collection, regex = FALSE)
if (is.null(paper_key)==TRUE){
#if there is no research paper id, create it and save it in the collection
paper_key = set_obkms("taxpub_research_paper", "research_paper")
save_to_mongo(key = paper_key, value = doi, type = "research_paper", collection = general_collection)
}
paper_id = identifier(paper_key)
article_id = identifiers$root_id
#query mongo for publisher id
publisher_lit = unlist(atoms$publisher)["text_value"]
publisher_key = check_mongo(value = publisher_lit, type = "publisher", collection = general_collection, regex = FALSE)
if (is.null(publisher_key)==TRUE){
#if there is no research paper id, create it and save it in the collection
publisher_key = set_obkms("taxpub_publisher", "publisher")
save_to_mongo(key = publisher_key, value = publisher_lit, type = "publisher", collection = general_collection)
}
publisher_id = identifier(publisher_key)
#query mongo for journal id
journal_lit = unlist(atoms$journal)["text_value"]
journal_key = check_mongo(value = journal_lit, type = "journal", collection = general_collection, regex = FALSE)
if (is.null(journal_key)==TRUE){
#if there is no research paper id, create it and save it in the collection
journal_key = set_obkms("taxpub_journal", "journal")
save_to_mongo(key = journal_key, value = journal_lit, type = "journal", collection = general_collection)
}
journal_id = identifier(journal_key)
tt = ResourceDescriptionFramework$new()
tt$add_triple(journal_id, rdf_type, Journal)
sapply(atoms$journal, function(j) {
tt$add_triple(journal_id, pref_label, j)
})
sapply(atoms$journal_abbrev, function(j) {
tt$add_triple(journal_id, alt_label, j)
})
sapply(atoms$issn, function(i) {
tt$add_triple(journal_id, issn, i)
})
sapply(atoms$eIssn, function(i) {
tt$add_triple(journal_id, eissn, i)
})
tt$add_triple(journal_id, frbr_part, article_id)
tt$add_triple(article_id, rdf_type, Article)
sapply(atoms$title, function(i) {
tt$add_triple(article_id, rdfs_label, i)
})
sapply(atoms$title, function(i) {
tt$add_triple(article_id, dc_title, i)
})
sapply(atoms$doi, function(i) {
tt$add_triple(article_id, has_doi, i)
})
sapply(atoms$publisher, function(i) {
tt$add_triple(article_id, has_publisher, i)
})
sapply(atoms$date, function(i) {
tt$add_triple(article_id, publication_date, i)
})
sapply(list(pub_date(atoms$pub_year, atoms$pub_month, atoms$pub_day)),
function(i) {
tt$add_triple(article_id, publication_date, i)
})
tt$add_triple(article_id, has_publisher_id, publisher_id)
tt$add_triple(article_id, realization_of, paper_id)
sapply(atoms$issue, function(i) {
tt$add_triple(article_id, has_issue, i)
})
sapply(atoms$keyword, function(i) {
tt$add_triple(identifiers$nid, has_keyword, i)
})
tt$add_triple(publisher_id, rdf_type, Publisher)
sapply(atoms$publisher, function(i) {
tt$add_triple(publisher_id, rdfs_label, i)
})
tt$add_triple(paper_id, rdf_type, Paper)
return(tt)
}
#' @export
keyword_group = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, KeywordGroup)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$keyword, function(i) {
tt$add_triple(identifiers$nid, has_keyword, i)
})
return(tt)
}
#' @export
abstract = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, Abstract)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
sapply(atoms$trans_abstract, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
title = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, Title)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
author_new = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
full_name = function(lsurname, lgiven_name) {
if (length(lsurname) == 1 && length(lgiven_name) == 1) {
paste(lgiven_name[[1]]$text_value, lsurname[[1]]$text_value)
}
else if (length(lsurname) == 1) {
lsurname[[1]]$text_value
}
else {
NA
}
}
atoms$full_name = ifelse(length(atoms$full_name) == 0, list(literal(full_name(atoms$surname,
atoms$given_names), xsd_type = rdf4r::xsd_string)), atoms$full_name)
aid = sapply(atoms$aff_id, function(a) {
as.integer(gsub("[^0-9.]", "", a$text_value))
})
paper_id = identifiers$root_id
author_id = identifiers$nid
#concatenate affiliation institution and city
all_affs = NULL
for(r in 1:length(atoms$all_affiliations_institutions)){
a = paste0(atoms$all_affiliations_institutions[[r]]$text_value, ",", atoms$all_affiliations_cities[[r]]$text_value)
a = literal(a, xsd_type = rdf4r::xsd_string)
all_affs[[r]] = a
}
tt = ResourceDescriptionFramework$new()
tt$add_triple(paper_id, creator, author_id)
tt$add_triple(author_id, rdf_type, Person)
sapply(atoms$full_name, function(j) {
tt$add_triple(author_id, rdfs_label, j)
})
sapply(all_affs[aid], function(j) {
tt$add_triple(author_id, has_affiliation, j)
})
sapply(atoms$email, function(j) {
tt$add_triple(author_id, has_email, j)
})
return(tt)
}
#' @export
introduction_section = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, Introduction)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
discussion = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, Discussion)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
treatment_new = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
#lookup_taxonomic_concept = query_factory(p_query = qlookup_taxonomic_concept_id,
# access_options = access_options)
#openbiodiv_taxonomic_concept_id = identifier_factory(fun = list(lookup_taxonomic_concept),
# prefixes = access_options$prefix, def_prefix = access_options$prefix["openbiodiv"], schema_name = schema_name, mongo_key = mongo_key)
treatment_id = identifiers$nid
#check mongo collection for treatments+tc (treatment frbf:realizationof taxonomicConcept)
treatment_collection = mongolite::mongo("treatment_collection")
key = check_mongo(value = treatment_id$id, type = names(mongo_key), collection = treatment_collection, regex = FALSE)
if (is.null(key)){
#if there is no tc realization of the treatment, create it
key = set_obkms("taxonomic_concept", names(mongo_key))
#save it both in the treatment collection and in the general collection
general_collection = mongolite::mongo("new_collection")
save_to_mongo(key, treatment_id$id, names(mongo_key), treatment_collection)
save_to_mongo(key, treatment_id$id, "taxonomic_concept", general_collection)
}
taxonomic_concept_id = identifier(id = key, prefix = prefix)
#taxonomic_concept_id = openbiodiv_taxonomic_concept_id(list(treatment_id))
tt = ResourceDescriptionFramework$new()
tt$add_triple(treatment_id, rdf_type, Treatment)
tt$add_triple(treatment_id, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(treatment_id, has_content, i)
})
tt$add_triple(taxonomic_concept_id, rdf_type, TaxonomicConcept)
tt$add_triple(taxonomic_concept_id, realization, treatment_id)
return(tt)
}
#' @export
nomenclature_citations = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, NomenclatureCitationsList)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
nomenclature = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
nomenclature_id = identifiers$nid
tt = ResourceDescriptionFramework$new()
tt$add_triple(nomenclature_id, rdf_type, Nomenclature)
tt$add_triple(nomenclature_id, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(nomenclature_id, has_content, i)
})
return(tt)
}
#' @export
materials_examined = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, MaterialsExamined)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
diagnosis = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
diagnosis_id = identifiers$nid
tt = ResourceDescriptionFramework$new()
tt$add_triple(diagnosis_id, rdf_type, Diagnosis)
tt$add_triple(diagnosis_id, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(diagnosis_id, has_content, i)
})
return(tt)
}
#' @export
distribution = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, Distribution)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
taxonomic_key = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, TaxonomicKey)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
figure = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
tt = ResourceDescriptionFramework$new()
tt$add_triple(identifiers$nid, rdf_type, Figure)
tt$add_triple(identifiers$nid, is_contained_by, identifiers$pid)
sapply(atoms$text_content, function(i) {
tt$add_triple(identifiers$nid, has_content, i)
})
return(tt)
}
#' @export
taxonomic_name_usage_new = function (atoms, identifiers, access_options, schema_name, mongo_key)
{
taxon_id = identifiers$nid
# print(taxon_id)
atoml_to_val = function(atoml)
{
if (length(atoml) > 0) {
return(atoml[[1]]$text_value)
}
else {
return (NA)
}
}
# identifiers
label = literal(get_scientific_name_or_tcl(kingdom = atoml_to_val(atoms$kingdom),
phylum = atoml_to_val(atoms$phylum),
class = atoml_to_val(atoms$class),
order = atoml_to_val(atoms$order),
family = atoml_to_val(atoms$family),
subfamily = atoml_to_val(atoms$subfamily),
genus = atoml_to_val(atoms$genus),
subgenus = atoml_to_val(atoms$subgenus),
species = atoml_to_val(atoms$species),
subspecies = atoml_to_val(atoms$subspecies),
authorship = atoml_to_val(atoms$authorship),
secundum_literal = atoml_to_val(atoms$secundum_literal)))
if (is.null(label) && length(atoms$verbatim) >= 1)
{
label = atoms$verbatim[[1]]
}
if (is.null(label))
{
return(ResourceDescriptionFramework$new())
}
if (length(atoms$verbatim_status) >= 1) {
atoms$status = list(verbstat2openbiodiv(atoms$verbatim_status[[1]]$text_value,
def_prefix = access_options$prefix))
}
rank = function(kingdom = NA, phylum = NA, class = NA, order = NA,
family = NA, subfamily = NA, genus = NA, subgenus = NA,
species = NA, subspecies = NA) {
arglist = list(Kingdom = kingdom, Phylum = phylum, Class = class,
Order = order, Family = family, Subfamily = subfamily,
Genus = genus, Subgenus = subgenus, Species = species,
Subspecies = subspecies)
identifier(id = names(arglist)[max(sapply(1:length(arglist),
function(index) {
ifelse(has_meaningful_value(arglist[[index]]),
index, 0)
}))], prefix = access_options$prefix)
}
atoms$taxonomic_rank = list(rank(kingdom = atoml_to_val(atoms$kingdom),
phylum = atoml_to_val(atoms$phylum), class = atoml_to_val(atoms$class),
order = atoml_to_val(atoms$order), family = atoml_to_val(atoms$family),
subfamily = atoml_to_val(atoms$subfamily), genus = atoml_to_val(atoms$genus),
subgenus = atoml_to_val(atoms$subgenus), species = atoml_to_val(atoms$species),
subspecies = atoml_to_val(atoms$subspecies)))
if (length(atoms$regularzied_genus) > 0) {
atoms$genus = atoms$regularzied_genus
}
#find the tnu_id by looking at mongo collection for tnus
tnu_collection = mongolite::mongo("tnus")
label = label[!is.null(label)]
paper_id = stringr::str_extract(identifiers$root_id$id, "([^\\/]*)$")
#HERE DO A REGEX SEARCH
mongo_tnu = check_mongo(paper_id, label$text_value, tnu_collection, regex = FALSE)
#if there is no tnu there, create it and save it
if (is.null(mongo_tnu)){
#create id and save the tnu
mongo_tnu = set_obkms(schema_name, "tnu")
label = as.character(label$text_value)
save_to_mongo(key = mongo_tnu, value = paper_id , type = label, collection = tnu_collection)
}
#if there is id, jsut take it
tnu_id = identifier(mongo_tnu)
todate = function(year, month, day) {
list(literal(paste(year[[1]]$text_value, month[[1]]$text_value,
day[[1]]$text_value, sep = "-"), xsd_type = rdf4r::xsd_date))
}
atoms$date = append(atoms$date, todate(atoms$pub_year, atoms$pub_month,
atoms$pub_day))
article_id = identifiers$root_id
parent_element_id = identifiers$pid
tt = ResourceDescriptionFramework$new()
tt$add_triple(tnu_id, rdf_type, TaxonomicNameUsage)
tt$add_triple(tnu_id, mentions, taxon_id)
tt$add_triple(tnu_id, is_contained_by, parent_element_id)
sapply(atoms$date, function(i) {
tt$add_triple(tnu_id, publication_date, i)
})
sapply(atoms$verbatim_status, function(i) {
tt$add_triple(tnu_id, has_taxonomic_status, i)
})
sapply(atoms$status, function(i) {
tt$add_triple(tnu_id, has_taxonomic_status_id, i)
})
tt$add_triple(taxon_id, rdf_type, ScientificName)
tt$add_triple(taxon_id, rdfs_label, label)
tt$add_triple(taxon_id, has_scientific_name, label)
sapply(atoms$kingdom, function(i) {
tt$add_triple(taxon_id, dwc_kingdom, i)
})
sapply(atoms$phylum, function(i) {
tt$add_triple(taxon_id, dwc_phylum, i)
})
sapply(atoms$class, function(i) {
tt$add_triple(taxon_id, dwc_class, i)
})
sapply(atoms$order, function(i) {
tt$add_triple(taxon_id, dwc_order, i)
})
sapply(atoms$family, function(i) {
tt$add_triple(taxon_id, dwc_family, i)
})
sapply(atoms$subfamily, function(i) {
tt$add_triple(taxon_id, dwc_family, i)
})
sapply(atoms$genus, function(i) {
tt$add_triple(taxon_id, dwc_genus, i)
})
sapply(atoms$subgenus, function(i) {
tt$add_triple(taxon_id, dwc_subgenus, i)
})
sapply(atoms$species, function(i) {
tt$add_triple(taxon_id, dwc_species_ep, i)
})
sapply(atoms$subspecies, function(i) {
tt$add_triple(taxon_id, dwc_subspecies_ep, i)
})
sapply(atoms$verbatim_rank, function(i) {
tt$add_triple(taxon_id, has_verbatim_rank, i)
})
sapply(atoms$taxonomic_rank, function(i) {
tt$add_triple(taxon_id, has_taxonomic_rank_id,
i)
})
sapply(atoms$authorship, function(i) {
tt$add_triple(taxon_id, dwc_authorship, i)
})
return(tt)
}
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